Algisphaera agarilytica gen nov, sp nov, a novel representative of the class Phycisphaerae within the phylum Planctomycetes isolated from a marine alga

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 105, Issue 2, 2014, Pages 317-324

  Yoon, Jaewoo ^a   Jang, Jae Hyuk ^b   Kasai, Hiroaki ^c  

^a Keimyung University   (South Korea)

^b Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^c KITASATO UNIVERSITY   (Japan)

Author keywords

16S rRNA gene; Algisphaera agarilytica gen nov, sp nov; Marine alga; Planctomycetes; Polyphasic taxonomy

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; CYTOSINE; DIAMINOPIMELIC ACID; FARNOQUINONE; FATTY ACID; GUANINE; RIBOSOME RNA;

ALGA; ALGISPHAERA AGARILYTICA; AMINO ACID ANALYSIS; ARTICLE; BACTERIAL CELL WALL; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CLADOPHORA; GENE SEQUENCE; LIPID COMPOSITION; MICROBIAL MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPIC VARIATION; PHYCISPHAERA MIKURENSIS; PHYCISPHAERAE; PHYLOGENY; PLANCTOMYCETES; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

AMINO ACIDS; AQUATIC ORGANISMS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CELL WALL; CHLOROPHYTA; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; GRAM-NEGATIVE BACTERIA; MICROSCOPY, ELECTRON, TRANSMISSION; MOLECULAR SEQUENCE DATA; PHYLOGENY; QUINONES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84893466781     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-013-0076-1     Document Type: Article

References (40)

1. Armstrong E, Rogerson A, Leftley JW (2000) The abundance of heterotrophic protists associated with intertidal seaweeds. Estuar Coast Shelf Sci 50:415-424
2. Atlas RM (1993) In: Parks LC (ed) Handbook of microbiological media. CRC, Boca Raton
3. Bartsch I, Wiencke C, Bischof K et al (2008) The genus Laminaria sensu lato: recent insights and developments. Eur J Phycol 43:1-86
4. Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049-1070
5. Blenden DC, Goldberg HS (1965) Silver impregnation stain for Leptospira and flagella. J Bacteriol 89:899-900
6. Brosius J, Palmer ML, Kennedy PJ, Noller HF (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75:4801-4805
7. Choi JH, Im WT, Liu QM, Yoo JS, Shin JH, Rhee SK, Roh DH (2007) Planococcus donghaensis sp nov, a starch-degrading bacterium isolated from the East Sea, South Korea. Int J Syst Evol Microbiol 57:2645-2650
8. Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2003) Molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant. Appl Environ Microbiol 69:7354-7363
9. Collins MD, Jones D (1981) A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 51:129-134
10. Derakshani M, Lukow T, Liesack W (2001) Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl Environ Microbiol 67:623-631
11. Elshahed MS, Youssef NH, Luo Q, Najar FZ, Roe BA, Sisk TM, Bühring SI, Hinrichs KU, Krumholz LR (2007) Phylogenetic and metabolic diversity of Planctomycetes from anaerobic, sulfide- and sulfur-rich Zodletone Spring, Oklahoma. Appl Environ Microbiol 73:4707-4716
12. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
13. Fitch WM (1971) Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406-416
14. Fuerst JA (1995) The Planctomycetes: emerging models for microbial ecology, evolution and cell biology. Microbiology 141:1493-1506
15. Fuerst JA (2004) Planctomycetes: a phylum of emerging interest for microbial evolution and ecology. WFCC Newsl 38:1-11
16. Fuerst JA (2005) Intracellular compartmentation in planctomycetes. Annu Rev Microbiol 59:299-328
17. Fuerst JA (2013) The PVC superphylum: exceptions to the bacterial definition? Antonie Van Leeuwenhoek 104:451-466
18. Fukunaga Y, Kurahashi M, Sakiyama Y, Ohuchi M, Yokota A, Harayama S (2009) Phycisphaera mikurensis gen nov, sp nov, isolated from a marine alga, and proposal of Phycisphaeraceae fam nov, Phycisphaerales ord nov and Phycisphaerae classis nov. in the phylum Planctomycetes. J Gen Appl Microbiol 55:267-275
19. Hansen GH, Sørheim R (1991) Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 13:231-241
20. Harper JJ, Davis GHG (1979) Two-dimensional thin-layer chromatography for amino acid analysis of bacterial cell walls. Int J Syst Bacteriol 29:56-58
21. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719-1728
22. Jetten MS, Niftrik Lv, Strous M, Kartal B, Keltjens JT, Op den Camp HJ (2009) Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol Biol 44:65-84
23. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
24. Köhler T, Stingl U, Meuser K, Brune A (2008) Novel lineages of Planctomycetes densely colonize the alkaline gut of soil-feeding termites (Cubitermes spp.). Environ Microbiol 10:1260-1270
25. König E, Schlesner H, Hirsch P (1984) Cell wall studies on budding bacteria of the Planctomyces/Pasteuria group and on a Prosthecomicrobium sp. Arch Microbiol 138:200-205
26. Lage OM, Bondoso J (2011) Planctomycetes diversity associated with macroalgae. FEMS Microbiol Ecol 78:366-375
27. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208-218
28. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159-167
29. Perry LB (1973) Gliding motility in some non-spreading flexibacteria. J Appl Microbiol 36:227-232
30. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
31. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, Newark
32. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407-477
33. Schlesner H, Stackebrandt E (1986) Assignment of the genera Planctomyces and Pirella to a new family Planctomycetaceae fam nov and description of the order Planctomycetales ord nov Syst Appl Microbiol 8:174-176
34. Staley JT, Fuerst JA, Giovannoni S, Schlesner H (1992) The order Planctomycetales and the genera Planctomyces, Pirellula, Gemmata and Isosphaera. In: Balows A, Trü per H, Dworkin M, Harder W, Schleifer KH (eds) The Prokaryotes: a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, 2nd edn. Springer, New York, pp 3710-3731
35. Storesund JE, Øvreås L (2013) Diversity of Planctomycetes in iron-hydroxide deposits from the Arctic Mid Ocean Ridge (AMOR) and description of Bythopirellula goksoyri gen nov, sp nov, a novel Planctomycete from deep sea iron-hydroxide deposits. Antonie Van Leeuwenhoek 104:569-584
36. Tamura K, Peterson D, Petersen N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using Maximum Likelihood, evolutionary distance, and Maximum Parsimony methods. Mol Biol Evol 28:2731-2739
37. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
38. Wang J, Jenkins C, Webb RI, Fuerst JA (2002) Isolation of Gemmata-like and Isosphaera-like planctomycete bacteria from soil and freshwater. Appl Environ Microbiol 68:417-422
39. Ward NL (2010) Family I. Planctomycetaceae Schlesner and Stackebrandt 1987, 179VP (Effective publication: Schlesner and Stackebrandt 1986, 175) emend. Ward (this volume). In: Krieg NR, Ludwig W, Whitman WB, Hedlund BP, Paster BJ, Staley JT, Ward N, Brown D (eds) The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, 2nd edn. Springer, New York, pp 879-925
40. Ward N, Staley JT, Fuerst JA, Giovannoni S, Schlesner H, Stackebrandt E (2006) The order Planctomycetales, including the genera Planctomyces, Pirellula, Gemmata and Isosphaera and the Candidatus genera Brocadia, Kuenenia and Scalindua. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The Prokaryotes: a handbook on the biology of bacteria, vol 7, 3rd edn. Springer, New York, pp 757-793